Dataset DOI: 10.5061/dryad.70rxwdcbf

Description of the data and file structure

In this study we combine measurements of light transmission through the darkly pigmented and translucent regions of male glow-worms’ pronotal shield with behavioural assays of the effects of UV/white light exposure to test the potential role of the pronotal shield in reducing the intensity of light reaching the compound eye, and it's behavioural implementation. We demonstrate that the pronotal shield of glow-worms acts as an extraretinal short wavelength filter for the dorsal compound eye.

Files and variables

File: Trackball_raw_data.zip

Description: Contains all videos that were manually analysed to obtain males' head position (retracted or extended from beneath the headshield) under different light conditions. Trials all include an initial control trial trial where males are presented with a dummy female (green LED), followed by a test trial where males are exposed to UV or white light. Both light condition are separated into two folders, each containing individual subfolders for all tested males.

Files description:

 For each males, folders contain:

• "Trackball_GW_cam[...].avi": the raw video file
• "Trackball_GW_cam[...].csv": a file containing the list of frames and timestamps of the video
• "Trackball_GW_LED_stim[...].csv": LED file corresponding to the timestamps of the light stimulation

Variables are described below when used in the relevant scripts in "Trackball_analysis.zip".

File: Trackball_analysis.zip

Description: This folder contains all the R scripts used to analyse the trackball data. The data folder contains the manually labelled frames for each video, indicating head position which is subsequently analysed in the script "03-Analysis.Rmd".

Subfolders & file description:

1. Code:
   • Data_preprocessing: Contains 3 scripts for pre-processing the raw data :
     • "00-Extract_frame_of_LED.Rmd": Extract the frames relevant to the current analysis from the camera file and merge with times of LED stimulation
     •  "01-Extract_CAM_file_before_after.Rmd": Create a file of the relevant frames with an empty column for "Head_position" to be filled in manually.
     • "02-Create_summary_files.Rmd": After manual entry of head position for each frames, this script creates summary files containing the retraction latency and duration per male per trial and averaged across all males.
   • "03-Analysis": .Rmd script to analyse glow-worms head position (output from script 02-). .html is the output of the plots.
2. Data:
   • "UV/" and "White/" folders: Contain the raw data obtained from the trackball. For each tested glow-worms, the folders contain 3 files :
     • "GW[...]_head_in_time.csv" and "GW[...]_LED.csv": Raw data from the trackball -containing the time of each frame, and from the LED stimulator -containing the time at which the LEDs where switched ON/OFF. Both the file are merged in script 00- to extract relevant frames. The relevant variables are described in below the "GW[...]_CAM_short.csv" and "GW[...]_UV_LED_frames.csv"  descriptions.
     • "GW[...]_CAM_short.csv" = the camera showing each frame and before manually assessing head location. Variables are:
       • GW = Glow-worm ID number
       • frame_nbr = the frame number
       • interframe_interval = the time between current frame and the previous frame (in seconds)
       • Time_norm = the time in seconds, normalised to the time the LED changes from green to white/UV.
       • Side = the side the green LED was presented (L/R for left or right)
       • LED = the colour of the LED currently ON (G for green, W for white and UV for ultraviolet)
       • head_position = empty column added for filling with manual assessment of head position.
     • "GW[...]_UV_LED_frames.csv":  contains the times at which the LEDs where switched ON/OFF, variables are:
       • LED = the colour and side of the LED currently ON (0 for all LEDs off, L/R or Left_green/Right_green for green on the left or the right side, W for white and Right_UV or Left_UV for ultraviolet)
       • Time_stamp = the time recorded by the LED stimulator
     • "Manual_analysis_time_head_out" "/UV" and "/White": Contains a copy of the previously generated "GW[...]_CAM_short.csv" files. Head position has been manually assessed and entered in the last empty column "head_position":
       • head_position = "i" for inside (i.e., retracted beneath the pronotal shield) and "o" for outside (i.e,. extended out from under the shield)
   • All other .csv files are collation or summaries of the previous files:
     • "UV_all_GW.csv" and "White_all_GW.csv": Collated data from all "GW_CAM_short.csv" files. One variable is added:
       • Head_status = head_position expressed as binary data (0 = head out, 1 = head in)
     • "UV_latency_summary.csv" and "White_latency_summary.csv": Summary table showing the time males spent with the head in or out of the pronotal shield in the different lighting conditions. Variables are:
       • Latency_to_head_retraction = average time before the male retracted the head under the pronotal shield (in seconds).
       • time_in_ctrl = time the male spent with the head retracted beneath the pronotal shield when the green light is on
       • time_out_ctrl = time the male spent with the head outside of the pronotal shield when the green light is on
       • time_in_alan = time the male spent with the head retracted beneath the pronotal shield when the white or UV light is on
       • time_out_alan = time the male spent with the head outside of the pronotal shield when the the white or UV light is on
3. "TB_head_retraction.Rproj": The R project used to read and run all scripts described above.

File: Spectrometry_data_and_analysis.zip

Description: This folder contains all the data and scripts used to analyse the optical measurement data. Raw data obtained by the powermeter and spectrometer are located at "Data/Power/" and "Data/Spectrum/" respectively. After preprocessing the raw data (scripts 00-, 01-, and 02-), analysis is done for the spectrum (script 03-) and power (script 04-).

Subfolders & file description:

1. Code:
   • Data_preprocessing: Contains 3 scripts for data pre-processing the raw data
     • "00-Extract_all_power_photon.Rmd": extracting power values in photons
     • "01-Calculate_photon_ratio_attenuation.Rmd" : calculating the photon attenuation ratio
     • "02-Extract_all_spectrum.Rmd": extracting the spectrums from the raw spectrometry data
   • "03-Spectrum_analysis": .Rmd script to analyse the spectrum output from script 02-. .html is the output of the plots.
   • "04-Power_analysis.Rmd": .Rmd script to analyse the power output from script 00- and 01-. .html is the output of the plots.
2. Data:
   • Power/Recordings: Contains all the raw power recordings for each glow-worm (GW) pronotal shield (.csv). In each GW folder, .csv files correspond to the recording of the tested wavelength, going through the control slide (S1) or the pronotal shield slide (S2). For the pronotal shield slides, loc_A corresponds to a recording in the light area of the pronotum, while loc_B corresponds to a recording in the dark area. Loc_A and loc_B in the S1 slides are the corresponding control recordings.
     • File name format: Male glow-worm ID number _ tested wavelength _ slide number _ powermeter wavelength setting _ recording location. NB : the recordings were all tested with both 200 nm (default powermeter setting) and the actual tested wavelength, only the later was used for analysis.
     • File content: the first few lines of the file are the settings of the powermeter. From line 15, variables are :
       • Samples: ID of the sampled point
       • Date
       • Time
       • Current (A)
       • Power (W)
       • Irradiance (W/cm²)
       • Power (dBm)
       • Saturation (%)
   • Spectrum/Recordings: Contains all the spectrum for each glow-worm (GW) pronotal shield at each tested wavelength. In each GW folder, .spf2 are the spectrum in the native trace format used by the ThorSpectra software, and the .txt files contain the raw points for use in analysis. Loc_A corresponds to a recording in the light area of the pronotum, while loc_B corresponds to a recording in the dark area.

     • File name format: Male glow-worm ID number _ tested wavelength _ recording location.

     • File content: For each narrowband LED and the white broad spectrum LED recorded at the same integration time, variables are :

       • V1, V3, V5, V7, V9, V11: Wavelength (nm)
       • V2, V8: Intensity control with LED off
       • V4, V6: Intensity measured through the control slide
       • V10, V12: Intensity measured through the pronotal shield.

       For recordings of the white broad spectrum LED, measured through the dark region only and with the maximum, integration time ("whitemax" files) variables are :

       • V1: Wavelength (nm)
       • V2: Intensity
   • All other files in the data folders are the power and spectrum data output obtained by processing the raw data using scripts 00-, 01- and 02- and are the ones used by the analysis script. Variables are described below (only the first time they appear) :
     • "All_GW_attenuation.csv" contains the mean percentage of attenuation for each GW at each wavelength, variables are:
       • gw = ID of the glow-worm
       • recording_area = dark or light recording area
       • tested_wavelength = the theoretical LED wavelength in nanometres.
       • percent_left = the percentage of light going through the pronotal shield compared to the control (%)
       • attenuation = the percentage of attenuation (100-percent_left, in %)
     • "All_GW_power_W.csv" and individual "GW[...]_power_W.csv":  contains the mean power for each GW at each wavelength, or the individual power recordings per GW, respectively. Variables have the same structure:
       • nm_setting = the wavelength setting of the powermeter, value is 200 nm (default) or the actual tested wavelenght. Only the actual values are used for the analysis.
       • test =  whether the value is from a control slide or the pronotal shield slide.
       • Time_sec = time in seconds
       • Power_W = Power in Watts
       • Photon_flux = in photon/seconds
     • "All_GW_spectrum_colours.csv" and  "All_GW_spectrum_whites.csv": all spectrums for all males. Variables are:
       • lamba = recorded wavelength in nanometers
       • off = Intensity control measured with LED off
       • ctrl: Intensity measured through the control slide
       • shield: Intensity measured through the pronotal shield.
   • "2025_Headshield_spectrometry.Rproj": The R project used to read and run all scripts described above.

Code/software

All analysis was performed in R 4.3.2. Packages used are indicated at the top of each script, and all scripts are annotated. Additional information can be found in the previous section describing each file.